Stoichiometric reactions of Pd(0) nanoparticles with various amounts of white phosphorus (P4) are an efficient route to convert them into the corresponding Pd phosphides PdxPy. Formation of crystallized palladium phosphide nanoparticles is a two-step process, which allows exploring in detail the phase transitions of the PdxPy system, from amorphous Pd–P nanoparticles (formed in a first step at moderate temperature) to crystallization (at higher temperature). The second temperature was found to be strongly dependent on the Pd/P ratio: PdP2, Pd5P2 and Pd3P stoichiometries form the amorphous phases, but only PdP2 and Pd5P2 could be further crystallized from them. Although it exists as a bulk crystalline material, Pd3P could only be crystallized by starting from the more Pd-rich Pd6P composition. Phase-to-phase transformations from P-poor phosphides (Pd3P and Pd5P2) to the P-rich PdP2 were also demonstrated, and a first Pd–P phase diagram at the nanoscale was tentatively produced.